SDR Deposit of the Week: Video tutorials for 4D visualization

May 15, 2017
Amy E. Hodge
Co-expression of CDT1A and SOL2 in Arabidopsis thaliana seedling leaf

Many researchers rely on open source software for data analysis, but lack of documentation on how to use the software can sometimes be an issue. In these situations, it's up to someone in the community to step up and create better resources to help people learn how to get the most out of these tools.

Stanford biology undergrad Nathan Cho found himself in just this situation recently while working on his honors thesis. Cho's project involved studying how stem cell development in plants affects the timing of the cell cycle, the process by which cells grow and divide. Analysis of his microscopy images required him to use open source software from the Max Plank Institute called MorphoGraphX.

"My PI (Dominique Bergmann) and I thought it would be helpful for other people, both in our lab and outside of it, if someone were to develop tutorials," said Cho. "I made a series of video tutorials that are publicly available, so that scientists can learn MorphoGraphX for their own projects."

Cho was required to deposit his honors thesis into the Stanford Digital Repository (SDR) and decided to deposit the video tutorials there as well, "because the SDR maintains a permanent location" for the content. "We want them to be publicly available for as long as people are using MorphoGraphX," indicated Cho, "and thus having them in a stable and secure location was important, and the SDR seemed like the perfect place for that."

We couldn't agree more! 

The SDR is an excellent place for all the products of your research endeavors that you'd like to make available to a broader audience. This includes videos, podcasts, presentations, and images, as well as data in all types of formats (really! all types!). You can deposit multiple files on a single item. Each item is assigned its own unique identifier and persistent URL (PURL). How you organize it all is up to you.

In this case, Cho and Professor Bergmann decided it would be best for each video to have its own PURL, "because we felt it would be easier from an accessibility standpoint," said Cho. "My tutorials address a range of different functions for MorphoGraphX, and someone trying to learn might not need to watch all of them." 

And with media streaming service available for SDR deposits, people can watch Cho's videos right on the PURL pages without even having to download them. The very first one is embedded below and available on its PURL page. Links to the other eight of Cho's video tutorials are near the bottom of that PURL page under "Related Items."